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=Star Alignment ([[Daniel:Notebook/Haplotyping/2014-1-31|Started 1/31/2014]])= [[Daniel:Notebook/Haplotyping|Back to Calendar]] ==PGP1_1-12 ([[Daniel:Notebook/Haplotyping/2014-1-31|Started 1/31/2014]])== Since the alignment on Friday went well, I'm now going to align the other lane, so I have data to try the rest of the HaploSeq algorithm with. '''Align PGP1_1-12_lane3.R2''' /home/k4zhang/softwares/STAR_2.3.0e.Linux_x86_64/STAR --runThreadN 8 --genomeDir /home/k4zhang/my_oasis_tscc/StarIndex/hg19 --readFilesIn /oasis/tscc/scratch/djacobse/haplotypeSeqData/fastq_files/PGP1_1-12.lane3.R2.fastq --outFileNamePrefix PGP1_1-12_lane3.R1 Note that I accidentally left the output as R1 (the first mate-pair). Fortunately, the actual R1 data is in a different folder, so this won't overwrite anything, and I'll change the name when the run is complete. Now I'll run the other lane (both mate-pairs), since clearly the run went well. '''Align PGP1_1-12_lane4.R1''' /home/k4zhang/softwares/STAR_2.3.0e.Linux_x86_64/STAR --runThreadN 8 --genomeDir /home/k4zhang/my_oasis_tscc/StarIndex/hg19 --readFilesIn /oasis/tscc/scratch/djacobse/haplotypeSeqData/fastq_files/PGP1_1-12.lane4.R1.fastq --outFileNamePrefix PGP1_1-12_lane4.R1 '''Align PGP1_1-12_lane4.R2''' /home/k4zhang/softwares/STAR_2.3.0e.Linux_x86_64/STAR --runThreadN 8 --genomeDir /home/k4zhang/my_oasis_tscc/StarIndex/hg19 --readFilesIn /oasis/tscc/scratch/djacobse/haplotypeSeqData/fastq_files/PGP1_1-12.lane4.R2.fastq --outFileNamePrefix PGP1_1-12_lane4.R2 ===Mate-Pair Aligning=== STAR advertises itself as able to accept mate pairs that are distally chromosomal, and even interchromosomal. This is because it is an RNASeq analyzer, and mate-pairs for exons may be quite far away from one another. As such, it would probably be even better than the HaploSeq method of singly aligning reads, followed by pairing, since STAR itself will align read pairs and requires no additional, in-house scripts (as the HaploSeq algorithm suggests). '''Mate-Pair Alignment of PGP1_1-12 Lane 3''' /home/k4zhang/softwares/STAR_2.3.0e.Linux_x86_64/STAR --runThreadN 8 --genomeDir /home/k4zhang/my_oasis_tscc/StarIndex/hg19 --readFilesIn /oasis/tscc/scratch/djacobse/haplotypeSeqData/fastq_files/PGP1_1-12.lane3.R1.fastq /oasis/tscc/scratch/djacobse/haplotypeSeqData/fastq_files/PGP1_1-12.lane3.R2.fastq --outFileNamePrefix PGP1_1-12_lane3.MP-R1R2
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